[gmx-users] MDP settings for No Temperature Coupling

[Justin Lemkul]

On 2/21/13 12:33 AM, bipin singh wrote:
> Hello All,
>
> I want to know how to mention a group (group2) without any temperature
> coupling in mdp file. From the manual I got to know that we should mention
> tau_t= -1 for no temperature coupling. And in the ref_temp section I have
> mention two values, 300K for coupled part (group1) and 10k for uncoupled
> part (group2). But my doubt is while generating velocities, which
> temperature I should mention in gen_temp section (i.e. 300K or 10K),
> because as far as I know we can not mention two different temperatures in
> gen_temp section while generating velocities. But ideally I want the
> uncoupled part to be at 10K and coupled part at 300K at the starting.
>
> Please let me know, which of the below scheme is correct for this purpose:
>
>
> * Method:1*
>
>   Tcoupl= V-rescale
>   tau_t= 0.1  -1
>   tc_grps= group1 group2
>   ref_t= 300  10
>   gen_vel= yes
>   gen_temp= 300
>
>
>   *Method:2*
>
>   Tcoupl= V-rescale
>   tau_t= 0.1  -1
>   tc_grps= group1 group2
>   ref_t= 300  10
>   gen_vel= yes
>   gen_temp= 10
>
>

I don't really see what difference it makes if the group is not actually 
regulated by the thermostat.  If it's not subjected to temperature coupling, you 
can't keep it at 10 K.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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